Thank you very much Justin for your quick answer.
Greetings
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Gro
On 12/24/13, 6:04 PM, David Saez wrote:
Dear all, I want to create a topology for S-adenosylmethionine using
AMBER99SB force field. I had to create some new atomtypes and, accordingly,
I have modified all the necessary files (atomtypes.atp, ffbonded,
ffnonbonded, etc). When I make
pdb2gmx -f s
Dear all, I want to create a topology for S-adenosylmethionine using
AMBER99SB force field. I had to create some new atomtypes and, accordingly,
I have modified all the necessary files (atomtypes.atp, ffbonded,
ffnonbonded, etc). When I make
pdb2gmx -f sam.pdb
I obtain a topol.top describing cor
Hi Facundo,
This is intended. The actual dihedral is a combination of two simpler types.
Cheers,
Tsjerk
On Tue, Dec 24, 2013 at 8:07 PM, fciocco wrote:
> Hi,
>
> I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb
> (gromos 54a7 FF) two different dihedrals are defined fo
Hi,
I'm not sure if this is a bug, but I have noted that in aminoacids.c.tdb
(gromos 54a7 FF) two different dihedrals are defined for the same set of
atoms:
for [ COO- ] C-termini:
[ dihedrals ]
N CA C O2 gd_45
N CA C O2 gd_42
and for [ COOH ]:
[ di
On 12/24/13, 2:38 AM, rbbioinfo wrote:
Hi, I want to plot the total displacement of an atom/ion along Z axis with
respect to time. Anybody kindly help me regarding how to calculate the
movement of any atom using gromacs. An early response will be highly
appreciated.
Sounds like a job for g_t
On 12/24/13, 9:59 AM, shahab shariati wrote:
Dear gromacs users
I used GridMAT-MD to obtain area per lipid and bilayer thickness.
I used vector for output_format in param_example file.
Based on the user guide for GridMAT-MD, when I used gnuplot:
perl convert_to_gnuplot.pl output.frame1.20
Dear gromacs users
I used GridMAT-MD to obtain area per lipid and bilayer thickness.
I used vector for output_format in param_example file.
Based on the user guide for GridMAT-MD, when I used gnuplot:
perl convert_to_gnuplot.pl output.frame1.20x20.average_thickness.dat 20 20
I encountered wi
Justin Lemkul wrote
> Gromacs reports energies in kJ per mole of equivalent systems. If you're
> looking for a value like configurational energy, use g_energy -nmol as
> needed to divide by the number of molecules in the system.
>
> -Justin
>
>
> On Mon, Dec 23, 2013 at 8:49 PM, virk <
> virkb
Just wondering, has anybody done a comparison with the Verlet scheme?
It could be useful to know whether it produces results consistent with
the 4.6 group scheme implementation or exhibits different behavior.
Cheers,
--
Szilárd
On Sun, Dec 22, 2013 at 1:08 AM, Lutz Maibaum wrote:
> On Dec 20, 2
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